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		<META NAME="Description" CONTENT="JDet: Interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures.">
		<META NAME="Keywords" CONTENT="JDet, Multiple alignment, sequence space, Conserved residues, function related, conservation, Xdet, S3det, CSBG, CNB">
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<a href="http://csbg.cnb.csic.es/">[Computational Systems Biology Group @CNB-CSIC]</a>
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			<h2><i>JDet</i> Home</h2>
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		<p>JDet  is a multiplatform software for the interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures. It contains the set of tools and features we consider critical for the daily work with this kind of data, and that previously were disseminated in different packages and web servers. The package includes two of our recently developed programs for extracting this kind of information from protein alignments. JDet can be extended via plugins to implement other methods or parse their results.</p>
		<p><center><img width="90%" src="img/jDet_features.png"/></center></p>
		<p>For a general description of the package and the biological problem which prompted its development, as well as more information on multiple sequence alignments (MSAs), conserved positions, specificity determining positions (SDPs), etc., please take a look at the following article: <a href="http://bioinformatics.oxfordjournals.org/content/28/4/584.full?etoc"> Muth <i>et al.</i> (2012). <i>Bioinformatics</i> <b>28</b> (4): 584-586.</a>; and the references cited there, specially <a href="http://www.ncbi.nlm.nih.gov/pubmed/16551661?dopt=Abstract">Pazos et <i>al.</i> (2006) <i>Bioinformatics</i>. <b>22(12):</b>1440-1448</a> and <a href="http://www.ncbi.nlm.nih.gov/pubmed/20133844">Rausell et <i>al.</i> (2010) <i>PNAS</i>. <b>107(5)</b>1995-2000</a>   </p>
		<h3>Download</h3>
		<p>	
			<ul>
				<li><u>Binaries</u>: <b> <a href="bin/JDet_1.4.5.zip">JDet_1.4.5.zip</a></b>. The .zip file contains a multiplatform distribution of <i>JDet</i> that was tested in recent versions of Linux, MS-Windows and Mac OSX. Command-line versions of <i>Xdet</i> and <i>S3Det</i> are also included (see below). This file also contains instalation instructions, examples and documentation.<br/>
					Previous releases:
					<ul>
						<li><a href="bin/JDet_1.4.4.zip">JDet_1.4.4.zip</a></li>						
						<li><a href="bin/JDet_1.4.3.zip">JDet_1.4.3.zip</a></li>
						<li><a href="bin/JDet_1.4.2-alpha.zip">JDet_1.4.2.zip</a></li>
						<li><a href="bin/JDet_1.4.1.zip">JDet_1.4.1.zip</a></li>
					</ul>
				</li>
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				<li><u>Source code</u>: <i>JDet</i> is open source under <a href="http://www.apache.org/licenses/LICENSE-2.0" target="_blank">Apache License 2.0</a>, and the code can be downloaded from <b><a href="http://code.google.com/p/jdet/">Google Code</a> </b>website. You are welcome to contribute to the project.
				</li>
				<br>
				<li><u>Plugins</u>: <i>JDet</i> can be extended with plugins writen in Java. Methods for extracting important positions from alignments, or filters for parsing method results can be added to <i>JDet</i> with this system. A plugin for parsing <a href="http://consurftest.tau.ac.il/">Conseq/Consurf<a> results is included with the distribution. We will maintain here a <b>repository of plugins</b> as more of these are developed. From a user point of view, installing plugins is just copying .jar files into JDet's directory. More information is given in the User Manual below. Here you can find <a href="http://csbg.cnb.csic.es/JDet/util/JDet-plugin-samples.zip">detailed <b>information for developers </b>on how to code plugins for <i>JDet</i></a>, including example code, etc. 
				</li>
			</ul>
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		<h3>Documentation</h3>
		<p>Here you can find on-line versions of the <b><a href="./JDet_help.html">user manual</a></b> and the <b><a href="./JDet_tutorial.html">guided tutorial</a></b>. These are also included in the dowloadable distribution.<br/>
		   <text style="color:red"><b> A list of <a href="./JDet_known_bugs.html">known bugs</a> is available, please read it.</b></text> If you want to report new bugs or be noticed about new versions and fixed bugs please send an email to Juan A. Garcia Martin (<img valign="bottom" src="img/email_jagarcia.png"/>). 
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		<h3>References</h3>
		<p>	Please cite the following reference when reporting any data or image generated with the program: <br/>
<ul><li><text style="font-size:12px;">
Thilo Muth, Juan A. Garcia-Martin, Antonio Rausell, David Juan, Alfonso Valencia & Florencio Pazos (2012).
JDet: Interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures. <a href="http://bioinformatics.oxfordjournals.org/content/28/4/584.full?etoc"> <i>Bioinformatics</i> <b>28</b>(4): 584-586.</a>
</text></ul></p>



		<h3>Included software and licenses</h3>
		<p>JDet includes binary distributions of two functional residue detection programs, <i>Xdet</i> and <i>S3Det</i>. These binaries can be also used outside the JDet environment, directly from the command line, e.g. for massive/batch runs (see Documentation above). 
			<ul>
				<li>
					<b><a href="http://pdg.cnb.uam.es/pazos/Xdet/">Xdet</a></b>
					<br/>
					<ul>
						<li><text style="font-size:12px;">Antonio del Sol, Florencio Pazos &amp; Alfonso Valencia.
							(2003). Automatic Methods for Predicting Functionally Important
							Residues. <I>Journal of Molecular Biology</I>. <B>326(4):</B>1289-1302.
							<a href="http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12589769&dopt=Abstract">[PubMed:12589769]</a> 
							<a href="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-47WBSCV-X&_user=217827&_coverDate=02%2F28%2F2003&_rdoc=24&_fmt=full&_orig=browse&_srch=%23toc%236899%232003%23996739995%23385689!&_cdi=6899&_sort=d&_docanchor=&_acct=C000011279&_version=1&_urlVersion=0&_userid=217827&md5=3919e6161d920fdbe69f9c8a978d0584">[HTML]</a> 
							<a href="http://pdg.cnb.uam.es/pazos/papers/treedet_jmb.pdf">[PDF]</a> </text>
							<br/>
						</li>
						 <li><text style="font-size:12px;">Florencio Pazos, Antonio Rausell & Alfonso Valencia. (2006).
							 Phylogeny-independent detection of functional residues.
							 <i>Bioinformatics</i>.
							 <b>22(12):</b>1440-1448.
							<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16551661&query_hl=1">[PubMed:16551661]</a> 
							<a href="http://bioinformatics.oxfordjournals.org/cgi/content/full/22/12/1440">[HTML]</a> 
							<a href="http://pdg.cnb.uam.es/pazos/papers/Xdet_Bioinformatics_06.pdf">[PDF]</a> </text>
						</li>						
					</ul>
					<br/>

						Command line versions of Xdet are also distributed independently of JDet. Binaries of Xdet for different architectures are available upon request. Contact Florencio Pazos (<img valign="bottom" src="img/email_pazos.png"/>).
					
					</text>
				</li>
				<br>
				<li>
					<b>S3det</b><br/>
					<ul>
					  <li>
					<text style="font-size:12px;">
						Antonio Rausell, David Juan, Florencio Pazos & Alfonso Valencia. (2010).
						Protein interactions and ligand binding: From protein subfamilies to functional specificity.
						<i>Proc Natl Acad Sci USA.</i> 
						<b>107(5):</b>1995-2000. 
						<a href="http://www.ncbi.nlm.nih.gov/pubmed/20133844">[PubMed:20133844]</a> 
						<a href="http://www.pnas.org/content/107/5/1995.abstract?etoc">[HTML]</a> 
						<a href="http://www.pnas.org/content/107/5/1995.full.pdf+html">[PDF]</a> 
						
					</text>
					</ul>
					<br/>

					Command line versions of S3det are also distributed independently of JDet. Binaries
 for different architectures as well as the source code are available upon request. Contact Antonio Rausell 
(<!-- <img valign="bottom" src="img/email_rausell.png"/> --> <font size=+1>antonio.rausell@isb-sib.ch</font>).
					  </ul>
				</li>
			</ul>
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		<p>JDet uses <b><a target="_blank" href="http://www.oracle.com/technetwork/java/javase/tech/index-jsp-138252.html">Java3D<sup><font size="-2">TM</font>,</sup></a></b> for <a href="http://download.java.net/media/java3d/builds/release/1.4.0_01/LICENSE-Java3D-v1_4_0.txt" target="_blank">research and instructional Use</a></p>
		<p>JDet also includes the <b><a href="http://www.jmol.org/">Jmol</a></b> plugin:  <text style="font-size:12px;">Jmol: an open-source Java viewer for chemical structures in 3D. <a target="_blank" href="http://www.jmol.org/">http://www.jmol.org/ </a></text></p>
		<p>Other third-party libraries are referenced in <a href="http://code.google.com/p/jdet/">JDet's site at Google Code</a></p>



		<h3>Contact</h3>
		<p>For general questions/queries about the software, please contact Florencio Pazos (<img valign="bottom" src="img/email_pazos.png"/>), for technical questions contact  Juan A. Garcia Martin (<img valign="bottom" src="img/email_jagarcia.png"/>).</p>

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<a href="http://csbg.cnb.csic.es/">[Computational Systems Biology Group @CNB-CSIC]</a>

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